The rice circadian clock orchestrates the rhizosphere microbiome to synchronize nitrogen supply with plant demand

Improving nitrogen use efficiency (NUE) is pivotal for sustainable agriculture but is limited by spatiotemporal mismatches between soil N supply and crop N demand. Here, we show that the rice circadian clock component Nhd1 coordinates rhizosphere microbial activity with plant diurnal N uptake. Nhd1 drives a rhythmic root exudation program: quercetin 3-gentiobioside peaks during the day against a constitutive baseline of baimaside secretion, both of which upregulate core microbial N-cycling genes to boost ammonium bioavailability. This Nhd1-orchestrated exudation rhythm aligns microbial N turnover with peak plant N demand. A synchronized microbial community engineered to match this diurnal N release pattern increased grain yield and NUE in field trials, with far greater benefits in cultivars harboring weak versus strong Nhd1 alleles. Our work uncovers a mechanism by which the plant circadian clock directly coordinates rhizosphere microbial functions to optimize N acquisition, thus providing a tractable strategy for sustainable crop production.